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Agonist efficiency from concentration-response curves: Structural implications and applications. Biophys J 2021; 120:1800-1813. [PMID: 33675765 DOI: 10.1016/j.bpj.2021.02.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 02/09/2021] [Accepted: 02/24/2021] [Indexed: 11/24/2022] Open
Abstract
Agonists are evaluated by a concentration-response curve (CRC), with a midpoint (EC50) that indicates potency, a high-concentration asymptote that indicates efficacy, and a low-concentration asymptote that indicates constitutive activity. A third agonist attribute, efficiency (η), is the fraction of binding energy that is applied to the conformational change that activates the receptor. We show that η can be calculated from EC50 and the asymptotes of a CRC derived from either single-channel or whole-cell responses. For 20 agonists of skeletal muscle nicotinic receptors, the distribution of η-values is bimodal with population means at 51% (including acetylcholine, nornicotine, and dimethylphenylpiperazinium) and 40% (including epibatidine, varenicline, and cytisine). The value of η is related inversely to the size of the agonist's headgroup, with high- versus low-efficiency ligands having an average volume of 70 vs. 102 Å3. Most binding site mutations have only a small effect on acetylcholine efficiency, except for αY190A (35%), αW149A (60%), and those at αG153 (42%). If η is known, the EC50 and high-concentration asymptote can be calculated from each other. Hence, an entire CRC can be estimated from the response to a single agonist concentration, and efficacy can be estimated from EC50 of a CRC that has been normalized to 1. Given η, the level of constitutive activity can be estimated from a single CRC.
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Nayak TK, Vij R, Bruhova I, Shandilya J, Auerbach A. Efficiency measures the conversion of agonist binding energy into receptor conformational change. J Gen Physiol 2019; 151:465-477. [PMID: 30635369 PMCID: PMC6445574 DOI: 10.1085/jgp.201812215] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 12/11/2018] [Indexed: 12/19/2022] Open
Abstract
Receptors alternate between resting↔active conformations that bind agonists with low↔high affinity. Here, we define a new agonist attribute, energy efficiency (η), as the fraction of ligand-binding energy converted into the mechanical work of the activation conformational change. η depends only on the resting/active agonist-binding energy ratio. In a plot of activation energy versus binding energy (an "efficiency" plot), the slope gives η and the y intercept gives the receptor's intrinsic activation energy (without agonists; ΔG0). We used single-channel electrophysiology to estimate η for eight different agonists and ΔG0 in human endplate acetylcholine receptors (AChRs). From published equilibrium constants, we also estimated η for agonists of KCa1.1 (BK channels) and muscarinic, γ-aminobutyric acid, glutamate, glycine, and aryl-hydrocarbon receptors, and ΔG0 for all of these except KCa1.1. Regarding AChRs, η is 48-56% for agonists related structurally to acetylcholine but is only ∼39% for agonists related to epibatidine; ΔG0 is 8.4 kcal/mol in adult and 9.6 kcal/mol in fetal receptors. Efficiency plots for all of the above receptors are approximately linear, with η values between 12% and 57% and ΔG0 values between 2 and 12 kcal/mol. Efficiency appears to be a general attribute of agonist action at receptor binding sites that is useful for understanding binding mechanisms, categorizing agonists, and estimating concentration-response relationships.
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Affiliation(s)
- Tapan K Nayak
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY
| | - Ridhima Vij
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY
| | - Iva Bruhova
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY
| | - Jayasha Shandilya
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY
| | - Anthony Auerbach
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY
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Geng Y, Magleby KL. Modal gating of endplate acetylcholine receptors: A proposed mechanism. ACTA ACUST UNITED AC 2017; 146:435-9. [PMID: 26621772 PMCID: PMC4664830 DOI: 10.1085/jgp.201511534] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Affiliation(s)
- Yanyan Geng
- Department of Physiology and Biophysics, University of Miami Miller School of Medicine, Miami, FL 33136
| | - Karl L Magleby
- Department of Physiology and Biophysics, University of Miami Miller School of Medicine, Miami, FL 33136
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Soh MS, Estrada-Mondragon A, Durisic N, Keramidas A, Lynch JW. Probing the Structural Mechanism of Partial Agonism in Glycine Receptors Using the Fluorescent Artificial Amino Acid, ANAP. ACS Chem Biol 2017; 12:805-813. [PMID: 28121133 DOI: 10.1021/acschembio.6b00926] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The efficacy of an agonist at a pentameric ligand-gated ion channel is determined by the rate at which it induces a conformational change from the resting closed state to a preopen ("flip") state. If the ability of an agonist to promote this isomerization is sufficiently low, then it becomes a partial agonist. As partial agonists at pentameric ligand-gated ion channels show considerable promise as therapeutics, understanding the structural basis of the resting-flip-state isomerization may provide insight into therapeutic design. Accordingly, we sought to identify structural correlates of the resting-flip conformational change in the glycine receptor chloride channel. We used nonsense suppression to introduce the small, fluorescent amino acid, 3-(6-acetylnaphthalen-2-ylamino)-2-aminopropanoic acid (ANAP), into specific sites in the extracellular and transmembrane domains. Then, under voltage-clamp conditions in Xenopus oocytes, we simultaneously quantified current and fluorescence responses induced by structurally similar agonists with high, medium, and low efficacies (glycine, β-alanine, and taurine, respectively). Analyzing results from nine ANAP-incorporated sites, we show that glycine receptor activation by agonists with graded efficacies manifests structurally as correspondingly graded movements of the β1-β2 loop, the β8-β9 loop, and the Cys-loop from the extracellular domain and the TM2-TM3 linker in the transmembrane domain. We infer that the resting-flip transition involves an efficacy-dependent molecular reorganization at the extracellular-transmembrane domain interface that primes receptors for efficacious opening.
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Affiliation(s)
- Ming S. Soh
- Queensland Brain
Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Argel Estrada-Mondragon
- Queensland Brain
Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Nela Durisic
- Queensland Brain
Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Angelo Keramidas
- Queensland Brain
Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Joseph W. Lynch
- Queensland Brain
Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
- School
of Biomedical Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
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5
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Michałowski MA, Kraszewski S, Mozrzymas JW. Binding site opening by loop C shift and chloride ion-pore interaction in the GABAAreceptor model. Phys Chem Chem Phys 2017; 19:13664-13678. [DOI: 10.1039/c7cp00582b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Molecular dynamics simulations of the shut α1β2γ2GABAAheteropentamer receptor homology model reveal significant differences between intersubunit interfaces (ligand binding G1, G2 and non-binding) compared to homomeric receptor assemblies and possible ion interaction sites in the top part of the transmembrane domain (TMD).
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Affiliation(s)
- M. A. Michałowski
- Laboratory of Neuroscience
- Department of Biophysics
- Wrocław Medical University
- ul. Chałubińskiego 3a
- 50-358 Wrocław
| | - S. Kraszewski
- Department of Biomedical Engineering
- Faculty of Fundamental Problems of Technology
- Wroclaw University of Science and Technology
- Wyb. Wyspiańskiego 27
- 50-370 Wrocław
| | - J. W. Mozrzymas
- Laboratory of Neuroscience
- Department of Biophysics
- Wrocław Medical University
- ul. Chałubińskiego 3a
- 50-358 Wrocław
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Gupta S, Chakraborty S, Vij R, Auerbach A. A mechanism for acetylcholine receptor gating based on structure, coupling, phi, and flip. J Gen Physiol 2016; 149:85-103. [PMID: 27932572 PMCID: PMC5217088 DOI: 10.1085/jgp.201611673] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 09/20/2016] [Accepted: 11/10/2016] [Indexed: 01/29/2023] Open
Abstract
Gupta et al. use single-channel electrophysiology to investigate the gating mechanism of acetylcholine receptor ion channels. They propose that channel opening starts at the M2–M3 linker and ligand-binding sites and proceeds through four brief intermediate conformations before ending with the collapse of a gate bubble. Nicotinic acetylcholine receptors are allosteric proteins that generate membrane currents by isomerizing (“gating”) between resting and active conformations under the influence of neurotransmitters. Here, to explore the mechanisms that link the transmitter-binding sites (TBSs) with the distant gate, we use mutant cycle analyses to measure coupling between residue pairs, phi value analyses to sequence domain rearrangements, and current simulations to reproduce a microsecond shut component (“flip”) apparent in single-channel recordings. Significant interactions between amino acids separated by >15 Å are rare; an exception is between the αM2–M3 linkers and the TBSs that are ∼30 Å apart. Linker residues also make significant, local interactions within and between subunits. Phi value analyses indicate that without agonists, the linker is the first region in the protein to reach the gating transition state. Together, the phi pattern and flip component suggest that a complete, resting↔active allosteric transition involves passage through four brief intermediate states, with brief shut events arising from sojourns in all or a subset. We derive energy landscapes for gating with and without agonists, and propose a structure-based model in which resting→active starts with spontaneous rearrangements of the M2–M3 linkers and TBSs. These conformational changes stabilize a twisted extracellular domain to promote transmembrane helix tilting, gate dilation, and the formation of a “bubble” that collapses to initiate ion conduction. The energy landscapes suggest that twisting is the most energetically unfavorable step in the resting→active conformational change and that the rate-limiting step in the reverse process is bubble formation.
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Affiliation(s)
- Shaweta Gupta
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY 14214
| | - Srirupa Chakraborty
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY 14214
| | - Ridhima Vij
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY 14214
| | - Anthony Auerbach
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY 14214
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Siekmann I, Fackrell M, Crampin EJ, Taylor P. Modelling modal gating of ion channels with hierarchical Markov models. Proc Math Phys Eng Sci 2016; 472:20160122. [PMID: 27616917 PMCID: PMC5014102 DOI: 10.1098/rspa.2016.0122] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 07/22/2016] [Indexed: 11/12/2022] Open
Abstract
Many ion channels spontaneously switch between different levels of activity. Although this behaviour known as modal gating has been observed for a long time it is currently not well understood. Despite the fact that appropriately representing activity changes is essential for accurately capturing time course data from ion channels, systematic approaches for modelling modal gating are currently not available. In this paper, we develop a modular approach for building such a model in an iterative process. First, stochastic switching between modes and stochastic opening and closing within modes are represented in separate aggregated Markov models. Second, the continuous-time hierarchical Markov model, a new modelling framework proposed here, then enables us to combine these components so that in the integrated model both mode switching as well as the kinetics within modes are appropriately represented. A mathematical analysis reveals that the behaviour of the hierarchical Markov model naturally depends on the properties of its components. We also demonstrate how a hierarchical Markov model can be parametrized using experimental data and show that it provides a better representation than a previous model of the same dataset. Because evidence is increasing that modal gating reflects underlying molecular properties of the channel protein, it is likely that biophysical processes are better captured by our new approach than in earlier models.
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Affiliation(s)
- Ivo Siekmann
- Systems Biology Laboratory, Melbourne School of Engineering, University of Melbourne, Melbourne, Australia
- Centre for Systems Genomics, University of Melbourne, Melbourne, Australia
| | - Mark Fackrell
- School of Mathematics and Statistics, University of Melbourne, Melbourne, Australia
| | - Edmund J. Crampin
- Systems Biology Laboratory, Melbourne School of Engineering, University of Melbourne, Melbourne, Australia
- Centre for Systems Genomics, University of Melbourne, Melbourne, Australia
- School of Mathematics and Statistics, University of Melbourne, Melbourne, Australia
- School of Medicine, University of Melbourne, Melbourne, Australia
- Australian Research Council Centre of Excellence in Convergent Bio-Nano Science and Technology, Melbourne, Australia
| | - Peter Taylor
- School of Mathematics and Statistics, University of Melbourne, Melbourne, Australia
- Australian Research Council Centre of Excellence for Mathematical and Statistical Frontiers, Melbourne, Australia
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Structural correlates of affinity in fetal versus adult endplate nicotinic receptors. Nat Commun 2016; 7:11352. [PMID: 27101778 PMCID: PMC4845029 DOI: 10.1038/ncomms11352] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 03/17/2016] [Indexed: 11/24/2022] Open
Abstract
Adult-type nicotinic acetylcholine receptors (AChRs) mediate signalling at mature neuromuscular junctions and fetal-type AChRs are necessary for proper synapse development. Each AChR has two neurotransmitter binding sites located at the interface of a principal and a complementary subunit. Although all agonist binding sites have the same core of five aromatic amino acids, the fetal site has ∼30-fold higher affinity for the neurotransmitter ACh. Here we use molecular dynamics simulations of adult versus fetal homology models to identify complementary-subunit residues near the core that influence affinity, and use single-channel electrophysiology to corroborate the results. Four residues in combination determine adult versus fetal affinity. Simulations suggest that at lower-affinity sites, one of these unsettles the core directly and the others (in loop E) increase backbone flexibility to unlock a key, complementary tryptophan from the core. Swapping only four amino acids is necessary and sufficient to exchange function between adult and fetal AChRs. Adult and fetal nicotinic acetylcholine receptors (AChRs) have different functional requirements and affinity for ACh. Here, the authors use molecular dynamics and electrophysiology to investigate this affinity, and identify four amino acids that when swapped exchange function between adult and fetal AChRs.
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